4. Data Sources and Methods 
We assembled causal (nutrient) and response variables (chlorophyll a , dissolved oxygen, water 
clarity, total suspended solids, macroalgae biomass, and submerged aquatic vegetation distribution) 
and physical data (temperature and salinity) at three spatial scales. Water quality data from Yaquina 
Estuary was compared to water quality data collected during the dry season for a set of seven Oregon 
estuaries for the purpose of estuarine classification (Section 4.2), and from a random sampling of all 
Oregon estuaries conducted as part of the EPA National Coastal Assessment (NCA) (Section 4.3). 
Historical data were assembled to assess whether there have been any long term trends in causal or 
response variables. For the trend analyses, we parsed the data into zones and seasons to minimize bias 
associated with differences in sampling (temporal or spatial). The zones are presented in Figure 2.1 
and discussed in Section 3.3, while the seasons are defined in Section 2.1. For details on the methods 
used and the quality assurance/quality control (QA/QC) of data used in this study see Appendix B. 
4.1 Yaquina Estuary Data 
4.1.1 Recent Data 
Data assembled for the Yaquina Estuary included recent (1998-2006) water quality cruises 
conducted by the Western Ecology Division, U.S. EPA. The sampling frequency and number of 
stations depended upon the year and month (Table 4.1). At each station, profiles of conductivity, 
temperature and depth (CTD; SBE 19 SEACAT Profiler, Sea-Bird Electronics, Inc, Bellevue, 
Washington), turbidity (Seapoint Turbidity Sensor, Seapoint Sensors, Inc., Kingston, New Hampshire), 
in situ fluorescence (WETStar Chlorophyll Fluorometer, WET Labs, Philomath, Oregon), and 
photosynthetically active radiation (PAR; PAR LI-193 underwater irradiance sensor, Lincoln, 
Nebraska) were measured. The profile measurements were taken at 0.5-sec intervals from the water 
surface to 0.5 m above the bottom, and during post-processing the data were binned into 0.25-m 
intervals. For the cruises conducted in 2006, dissolved oxygen was measured at surface, mid-depth, 
and bottom using a YSI multiparameter sonde (YSI 6600 EDS, YSI Inc., Yellow Springs, OH). At 
each station, water samples were collected, which were analyzed for dissolved inorganic nutrients 
- - + 3- 
(N0 3 + N0 2 , NH 4 , P0 4 and Si(OH) 4 ). During the 2006 cruises, additional water samples were 
collected and analyzed for total nitrogen (TN) and total phosphorous (TP). Water samples were 
collected for chlorophyll a analysis at each cruise location quarterly during 2002 and 2003 (surface 
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